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* Hdf5 1 12 doxygen merge (#615)Allen Byrne2021-05-041-33/+13
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 fix tools test for plugins * sync fork * Merge of changes from dev * Move problem option to bottom of the list until fixed * HDFFV-11106 - fix parsing optional args * HDFFV-11106 add note * grammer fix * Whitespace after clang formatting * Undo format version 11 changes * Update check to working version * Merge workflow and minor changes from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge serval small changes from dev * fix typo * Minor non-space formatting changes * GH #386 copyright corrections for java folder * revert because logic requires false return * Merges from develop #358 patches from vtk #361 fix header guard spelling * Remove case statement for H5I_EVENTSET * Correct call with versioning * Remove tabs * Double underscore change * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings Remove more underscores from header guards * Merge #380 from develop * Correct date entry * Split format source and commit changes on repo push * remove pre-split setting * Change windows TS to use older VS. * HDFFV-11212 JNI export util and Javadoc * Suggested review changes * Another change found * Committing clang-format changes * Some Javadoc warning fixes * Committing clang-format changes * Updated javadoc fixes * HDFFV-11228/9 merges from develop * remove obsolete debug comment * Fix conflict * HDFFV-11229 merge changes from develop * HDFFV-11229 merge second compare from develop * HDFFV-11229 fix reference file * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * Update with changes from develop * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Whitespace changes * Rework CMake add_custom to use the BYPRODUCTS argument * Revert CMake configure checks for round defines * With VS 2015 minimum strdup is supported * Doxygen comments merged from develop * doxygen build updates * Correct version string for map functions Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1 12 merges from develop (#412)Allen Byrne2021-03-031-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 fix tools test for plugins * sync fork * Merge of changes from dev * Move problem option to bottom of the list until fixed * HDFFV-11106 - fix parsing optional args * HDFFV-11106 add note * grammer fix * Whitespace after clang formatting * Undo format version 11 changes * Update check to working version * Merge workflow and minor changes from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge serval small changes from dev * fix typo * Minor non-space formatting changes * GH #386 copyright corrections for java folder * revert because logic requires false return * Merges from develop #358 patches from vtk #361 fix header guard spelling * Remove case statement for H5I_EVENTSET * Correct call with versioning * Remove tabs * Double underscore change
* Update URL in source file Copyright headers for web copy of COPYINGLarry Knox2021-02-201-1/+1
| | | | file - src and test directories.
* Basic alignment with async branch (#115) (#137)Quincey Koziol2020-11-301-70/+65
| | | | | | | * Basic alignment with async branch - trivial changes to reduce clutter in overall diff. * Update minor error code to reflect change within library * Update the error output to match library
* Merge available RM doxygen from develop to hdf5 1 12 (#131)Larry Knox2020-11-261-86/+1949
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Snapshot version 1.12 release 1-3. Update version to 1.12.1-4. * First cut of the H5 public API documentation. (#80) * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Full set of current H5F documentation. (#105) * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Migrated documentation for SWMR functions. * Catching up on MDC functions. * Integrated the H5F MDC function documentation. * Added MDC and parallel H5F functions. * Slightly updated main page. * Added doxygen/dox/H5AC_cache_config_t.dox to MANIFEST. * Doxygen - added (mostly) beginner functions (#112) * Doxygen - added (mostly) beginner functions * Removed duplicate H5Pset_szip function * Add src/H5module.h to MANIFEST. Co-authored-by: Gerd Heber <gheber@hdfgroup.org> Co-authored-by: bljhdf <58825073+bljhdf@users.noreply.github.com>
* Source formattedAllen Byrne2020-10-011-125/+111
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* Add clang-format changes from develop.Allen Byrne2020-09-281-7/+9
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* Clean up private / package / static namespace issues (function naming, whichQuincey Koziol2020-08-221-1/+1
| | | | | | header file, FUNC_ENTER / LEAVE, etc). Removed remaining personal email addresses from library source code (still needs cleaned from other directories). Misc. warning, style, and whitespace cleanup.
* Squashed commit of the token_refactoring branch:Dana Robinson2020-01-191-35/+89
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* Normalization with vol_integration (misc internal and datatype)Dana Robinson2018-09-201-2/+2
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* Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-2/+19
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* Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-251-6/+4
| | | | | | | | | | hdf5_1_10 * commit '54957d37f5aa73912763dbb6e308555e863c43f4': Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes. Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh. Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1 Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
* [svn-r25496] Description:Quincey Koziol2014-07-301-1/+1
| | | | | | | | | Merge 64-bit ID changes from branch to trunk. (Plus a few minor cleanups that aren't on the branch) Tested on: Mac OSX/64 10.9.4 (amazon) w/C++ & FORTRAN (h5committested on branch already for a week)
* [svn-r25399] bug fixes where a wrong type was used instead of hid_t.Mohamad Chaarawi2014-07-091-1/+1
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* [svn-r16281] Purpose: Add functions to allow more flexible traversal of ↵Neil Fortner2009-01-081-1/+6
| | | | | | | | | | | external links. Description: Added H5Pset/get_elink_cb to allow the user to specify a callback function to be called whenever an external link is traversed. Added H5Pset/get_elink_acc_flags to allow the user to specify the file access flags to use to open the target file of an external link. All these properties are set on a LAPL. Tested: jam, linew, smirom (h5committest)
* [svn-r15628] Description:Quincey Koziol2008-09-161-1/+1
| | | | | | | | | | | | | Remove trailing whitespace from C/C++ source files, with the following script: foreach f (*.[ch] *.cpp) sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f end Tested on: Mac OS X/32 10.5.5 (amazon) No need for h5committest, just whitespace changes...
* [svn-r14285] Description:Quincey Koziol2007-11-241-0/+2
| | | | | | | | | | | | | | | | | | | | | | | Add H5Lvisit() API routine. Add explicit regression tests for H5Lvisit_by_name(). Correct error with visiting links when links contain loop to group already encountered. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14284] Description:Quincey Koziol2007-11-241-0/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Add H5Lvisit_by_name() API routine to library. Eliminated all (five!) other group traversal routines and changed them all to use the new API routine. Cleaned up output of h5ls & h5stat: - Issue error when requesting recursive traversal of a file with the "group info" flag, but no group given - Print info about root group in all(?) appropriate situations - Don't print "verbose" information about root group until the root group is in the list of objects to display (mostly because h5ls & h5stat had a different twist on traversing the groups in a file that the other utilities) Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14228] Description:Quincey Koziol2007-11-011-2/+0
| | | | | | | | | | | | | | | | | Change H5Llink to H5Olink, which makes more sense. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14224] Description:Quincey Koziol2007-10-301-2/+4
| | | | | | | | | | | | | | | | | | | Change H5Literate -> H5Literate_by_name and add simpler form of H5Literate, to bring this routine into alignment with the other new API routines. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14117] Description:Quincey Koziol2007-08-281-2/+2
| | | | | | | | | | Move H5Glink() into "deprecated routines" section, replacing internal usage with H5Lcreate_hard/H5Lcreate_soft. Tested on: FreeBSD/32 6.2 (duty) FreeBSD/64 6.2 (liberty) Solaris/32 5.10 (linew)
* [svn-r13580] Description:Quincey Koziol2007-04-031-9/+15
| | | | | | | | | | | | Add version # and flags to external link format (as fields in a single byte), in order to accomodate future changes/expansions. Tested on: Mac OS X/32 10.4.9 (amazon) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2) FreeBSD/32 6.2 (duty) FreeBSD/64 6.2 (liberty)
* [svn-r13520] Description:Quincey Koziol2007-03-161-0/+1
| | | | | | | | | Added H5Lexists() API routine, which determines if a link of a particular name exists in a group. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13272] Description:Quincey Koziol2007-02-081-12/+11
| | | | | | | | Checkpoint attribute creation order coding on "by index" routines. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13253] Updated all C and C++ style source code files with the THG ↵Albert Cheng2007-02-071-2/+3
| | | | | | | | | copyright notice. Tested platform: Kagiso only since it is only a comment block change. If it works in one machine, it should work in all, I hope. Still need to check the parallel build on copper.
* [svn-r13248] Description:Quincey Koziol2007-02-061-1/+1
| | | | | | | | | More progress on creation order for attribbutes - they are now basically working for "compact" attribute storage. Tested on: FreeBSD/32 6.2 (duty) Mac OS X/32 10.4.8 (amazon)
* [svn-r13045] Description:Quincey Koziol2006-12-121-16/+5
| | | | | | | | | | | | | | Switch from using H5L_index_t/H5L_INDEX_<foo> to H5_index_t/H5_INDEX_<foo> in order to accommodate indices on aspects of attributes as well as links. Add basic support for deleting attributes in dense storage (needs more support/tests for shared attributes in dense storage still). Misc. cleanups, etc. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12932] Description:Quincey Koziol2006-11-171-4/+11
| | | | | | | | | | | | Basic support for H5Literate() routine. Still needs to be fleshed out and refactored to simplify. Also, needs tests. :-) Tested on: FreeBSD/32 4.11 (sleipnir) Linux/32 2.4 (heping) Linux/64 2.4 (mir) AIX/32 5.? (copper) Mac OS X/32 10.4.8 (amazon)
* [svn-r12906] Description:Quincey Koziol2006-11-131-1/+1
| | | | | | | | | | | | | | | | Straighten out some convoluted code when links were being deleted, which could cause the "delete" callback for user-defined links to not get called when the group they were in was deleted. Had to compromise on the "delete" callback though - only calls the callback with the ID for the file the link is in, instead of the group, since the group is being held open upstream in the calling sequence during a group deletion and this prevents a group and its ID from being created. (This could possibly be worked around, but would cause a fair bit of havoc in the code and I'm not entirely certain it's worth it...) Tested on: Linux/32 2.6 (chicago)
* [svn-r12895] Description:Quincey Koziol2006-11-131-2/+7
| | | | | | | | | | | | | Add new H5Lget_val_by_idx() routine & tests. Also includes most of changes for H5Ldelete_by_idx() routine. Tested on: Mac OS X/32 10.4.8 (amazon) FreeBSD/32 4.11 (sleipnir) Linux/32 2.4 (heping) Linux/64 2.4 (mir) AIX/32 5.? (copper)
* [svn-r12894] Description:Quincey Koziol2006-11-121-0/+3
| | | | | | | | | | | | Add H5Lget_name_by_idx routine & tests Move more H5G routines to deprecated API file Tested on: FreeBSD/32 4.11 (sleipnir) w/threadsafe Linux/32 2.4 (heping) C++ & FORTRAN Linux/64 2.4 (mir) w/build-all & enable_compat1.6 AIX/32 5.? (copper) w/parallel & FORTRAN
* [svn-r12878] Description:Quincey Koziol2006-11-071-1/+1
| | | | | | | | Flesh out support for looking up link info by index, some cases for using dense storage are working now. Tested on: Linux/32 2.6 (chicago)
* [svn-r12872] Description:Quincey Koziol2006-11-071-0/+15
| | | | | | | | | | | | Implement basic framework for H5Lget_info_by_idx and get it working for creation order indices on compact groups. Clean up code a bit. Close resource link in user-defined link traversal. Tested on: Linux/32 2.6 (chicago)
* [svn-r12865] Description:Quincey Koziol2006-11-061-1/+1
| | | | | | | Change name of H5Lunlink to H5Ldelete, per our design meeting last Friday. Tested on: Linux/32 2.6 (chicago)
* [svn-r12864] Description:Quincey Koziol2006-11-061-4/+5
| | | | | | | | Changed H5Lget_linkval() to H5Lget_val(), per our design discussion last Friday afternoon. Tested on: Linux/32 2.6 (chicago)
* [svn-r12835] Description:Quincey Koziol2006-10-311-4/+4
| | | | | | | | | Change H5Lget_linkinfo() to H5Lget_info() to better align with coming API changes. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r12832] Description:Quincey Koziol2006-10-301-11/+24
| | | | | | | | | | Clean up formatting and re-organize a bit... Tested on: Max OS X/32 10.4.8 (amazon) FreeBSD/32 4.11 (sleipnir) Linux/32 2.4 (heping) Linux/64 2.4 (mir)
* [svn-r12831] Changed the API for "unpacking" an external link value to take ↵James Laird2006-10-301-2/+2
| | | | | | | | | | the size of the linkval buffer, per Elena and Frank's suggestions while revising the documentation. Added error checking using this size, as well as a couple of tests. Tested on juniper, kagiso, and sol.
* [svn-r12700] Alert:Quincey Koziol2006-10-021-26/+32
| | | | | | | | | | | | | | | | | | | | | | | | | | | | File format is not stable, don't keep files produced! Description: First stage of checkins modifying the format of groups to support creation order. Implement "dense" storage for links in groups. Try to clarify some of the symbols for the H5L API. Add the H5Pset_latest_format() flag for FAPLs, to choose to use the newest file format options (including "dense" link storage in groups) Add the H5Pset_track_creation_order() flag for GCPLs, to enable creation order tracking in groups (although no index on creation order yet). Remove --enable-group-revision configure flag, as file format issues are now handled in a backwardly/forwardly compatible way. Clean up lots of compiler warnings and other minor formatting issues. Tested on: FreeBSD/32 4.11 (sleipnir) w/threadsafe Linux/32 2.4 (heping) w/FORTRAN & C++ Linux/64 2.4 (mir) w/enable-v1.6 compa Mac OSX/32 10.4.8 (amazon) AIX 5.3 (copper) w/parallel & FORTRAN
* [svn-r12608] Checked in External Link C examples.James Laird2006-08-221-2/+2
| | | | | | | | Since these examples need to follow filesystem paths, the Makefiles need to create directories in the examples directory; added this to the Makefile.am. Tested on Windows, mir, juniper
* [svn-r12528] Added User-Defined links to the library.James Laird2006-08-021-20/+88
| | | | | | | | | | | | | | Users can create external links using H5L_create_external(). These links point to an object in another HDF5 file. Users can alter the behavior of external links or create new kinds of links by registering callbacks using the H5L interface. Added tests, tools support, etc. Also a number of other, minor changes have been made (some restructuring of the H5L interface, for instance). Additional documentation and examples are forthcoming.
* [svn-r12452] Purpose:James Laird2006-07-051-0/+78
Feature Description: Revised Link APIs. Solution: New link APIs use H5L* H5*create_expand do not create links to the objects created; this must be done manually with H5Llink. Added APIs to link an object given its ID (H5Llink), to copy links (H5Lcopy), and changed creation APIs (H5Lcreate_hard and H5Lcreate_soft) and query API (H5Lget_linkinfo instead of H5Gget_objinfo). All old APIs are still supported in H5Gdeprec.c . Platforms tested: sol, mir, copper Misc. update: Forgot to update MANIFEST and release docs. Will do after checkin.